The present invention relates to a DNA microarray (DNA chip) which specifically reacts with a biochemical specimen and which is used for inspection equipment represented, for example, by a biochip to be used in order to obtain information on a structure of the specimen, especially in which several thousand to not less than ten thousand kinds of different types of DNA fragments are aligned and fixed at a high density as spots on a base plate such as a microscopic glass slide.
The method of analyzing the genetic structure has been remarkably progressed in recent years. A large number of genetic structures represented by those of human genes have been clarified. The analysis of the genetic structure uses a DNA microarray (DNA chip) in which several thousand to not less than ten thousand kinds of different types of DNA fragments are aligned and fixed as spots on a base plate such as a microscopic glass slide.
In recent years, there is a demand for enhancing the reproducibility, the quantitative performance in the information obtained from the DNA microarray and obtaining much more information from the DNA microarray. The information obtained from respective spots needs to be correct, uniform, and complex.
Those widely used as the method of forming the spots for the production of the DNA microarray are generally based on a system such as the QUILL system, the pin and ring system, and the spring pin system in which a sample solution containing DNA fragments is supplied (stamped) onto the base plate by using a so-called pin. When any one of the foregoing methods is adopted, it is important to suppress the dispersion of the volume and the shape of each spot so that the distance between the respective spots is maintained to be constant.
On the other hand, in order to realize a higher density, it is also greatly expected to develop a new method which is excellent in productivity and in which the shape control performance for the spot is satisfactory.
The conventional method of forming the spot is based on the supply (stamping) of the sample solution onto the base plate by using the pin. Therefore, the shape of the spot is diversified, for example, due to the shape of the forward end of the pin and/or the residue of the sample solution remaining at the forward end of the pin after the supply. As shown in FIG. 18, spots 200, each of which has many irregularities at the outer circumferential portion, are formed on a base plate 202.
When unknown DNA is inspected by using a DNA microarray arranged with a large number of spots having dispersed shapes, it is apt to be difficult to recognize the fluorescence light emission from the spot with a CCD camera or the like. Therefore, the inspection accuracy may be lowered.
Further, when many irregularities exist at the outer circumferential portion, the sample solution flows through angular portions. Therefore, the sample solutions in the plurality of spots 200 may be mixed with each other.
The present invention has been made taking the foregoing problems into consideration, an object of which is to provide a DNA microarray which makes it possible to improve the inspection accuracy for genetic analyses and which makes it possible to increase the amount of information to be obtained.
Another object of the present invention is to provide a DNA microarray which makes it possible to achieve a high degree of concentration of spots and which makes it possible to perform detailed genetic analyses.
Still another object of the present invention is to provide a DNA microarray which makes it possible to recognize the degree of the reaction with respect to an amount of DNA fragments immobilized in a spot and which makes it possible to obtain an analog inspection result for a specimen, in addition to a digital inspection result to indicate whether or not the reaction occurs.
The applicable range of the present invention is not limited to the DNA microarray in which DNA fragments are aligned and immobilized as spots. The present invention is generally usable for every type of the biochip which specifically reacts with a biochemical specimen and which is used in order to obtain information on the structure of the specimen.
The present invention lies in a biochip comprising a large number of spots based on capture solutions arranged on a base plate, obtained by supplying, onto the base plate, a plurality of types of the capture solutions each of which specifically reacts with a specimen and each of which is used to obtain information on a structure of the specimen; wherein a plurality of the spots, which have different spot sizes, are formed on the base plate.
Accordingly, it is possible for the respective spots to suppress the dispersion of the ability to capture the specimen among the spots, which would be otherwise caused by the difference in amount of the capture immobilized on the spot or by the different abilities of the captures to capture the specimen. Thus, it is possible to suppress the dispersion of inspection results and the deterioration of quantitative performance, which would be otherwise caused by the difference in detection sensitivity among the spots.
That is, the spot, which corresponds to the capture with a small amount to be immobilized on the base plate or which corresponds to the capture with a low ability to capture the specimen, is increased in size, generally in diameter of a circular configuration. Accordingly, the detection sensitivity per one spot can be increased. As a result, it is possible to uniformize the detection sensitivities of all of the spots.
In another aspect, the present invention has the following feature. That is, when a plurality of the spots are formed for captures of an identical type on a single sheet of the base plate, then the plurality of the spots, which have different spot sizes on the base plate respectively, are formed for the captures of the identical type.
When the construction as described above is adopted, it is possible to recognize the degree of the reaction corresponding to the size of the spot, in addition to a digital inspection result to indicate whether or not the reaction occurs with respect to the captures of the identical type. Thus, it is possible to obtain an analog inspection result for the specimen. Of course, the analog inspection result can be theoretically obtained by detecting, in an analog manner, the amount of a probe which reacts with the capture immobilized in one spot. However, actually, such a procedure cannot be executed due to the restriction including, for example, the detection sensitivity of the detection equipment, the resolution, and the reaction efficiency. Therefore, the analog analysis can be performed by combining the plurality of spots using the plurality of spots having the different sizes of the spots on the base plate respectively for the captures of the identical type as performed in the present invention, although the detection of a each spot is performed in a digital manner.
In still another aspect, the present invention lies in a biochip comprising a large number of spots based on capture solutions arranged on a base plate, obtained by supplying, onto the base plate, a plurality of types of the capture solutions each of which specifically reacts with a specimen and each of which is used to obtain information on a structure of the specimen; wherein a plurality of the spots are formed, in which an amount of a capture per unit area immobilized in each of the spots differs.
Accordingly, it is possible for the respective spots to suppress the dispersion of the ability to capture the specimen among the spots, which would be otherwise caused by the different abilities of the captures to capture the specimen, in the same manner as in the case in which the sizes of the spots differ as described above. Thus, it is possible to suppress the dispersion of inspection results and the deterioration of quantitative performance, which would be otherwise caused by the difference in detection sensitivity among the spots. That is, the concentration of the capture solution to be supplied is increased for the spot which corresponds to the capture with a low ability to capture the specimen. Accordingly, the amount of the capture immobilized on the spot is increased per unit area, and the detection sensitivity per one spot is increased. As a result, it is possible to uniformize the detection sensitivities of all of the spots.
The method of changing the amount per unit area of the capture amount immobilized on one spot may be also carried out by changing the concentration of the capture solution to be supplied as described above. Alternatively, the method may be also carried out by changing the capture amount to be supplied to one spot.
There is a certain upper limit for the capture amount immobilized per one spot. Therefore, the capture solution having a concentration lower than an average of all spots, or the capture solution in an amount smaller than an average of all spots is supplied for the spot corresponding to the capture having the high ability to capture the specimen. On the other hand, the capture solution at a concentration and/or in an amount corresponding to the upper limit of the capture amount to be immobilized or corresponding to an amount exceeding the upper limit is supplied to the spot corresponding to the capture having the low ability to capture the specimen.
Mistakes tend to be caused when the concentration and the amount of the capture solution to be supplied are individually managed for the respective spots as described above. It is advantageous to simplify the step to be as simple as possible. In such a case, when the capture solution is supplied onto the base plate by using an ink-jet method as described later on, it is preferable that the amount of solution to be supplied is changed by changing the number of discharge times for one spot.
The method of suppressing the dispersion of the ability to capture the specimen among the spots caused by the captures having the different abilities to capture the specimen by changing the concentration of the capture solution to be supplied or by changing the amount of the capture to be supplied for one spot is also used to reduce the dispersion when the immobilization ratio of the capture to be immobilized per one spot differs.
That is, as for the formation of the spot corresponding to the capture having the low immobilization ratio, it is possible to suppress the dispersion of the immobilization efficiency among the respective spots by increasing the concentration of the capture solution to be supplied, or by increasing the amount of the capture solution to be supplied per one spot.
In still another aspect of the present invention, when a plurality of spots of the captures of an identical type are formed on one sheet of the base plate, the plurality of the spots, which have different amounts of the capture per unit area immobilized on the base plate respectively, are formed for the captures of the identical type.
When the construction as described above is adopted, it is possible to recognize the degree of the reaction corresponding to the amount of the capture immobilized per unit area of the spot, in addition to a digital inspection result to indicate whether or not the reaction occurs with respect to the capture, concerning the captures of the identical type in the same manner as in the case in which the sizes of the spots differ as described above. Thus, it is possible to obtain an analog inspection result for the specimen. Of course, the analog inspection result can be theoretically obtained by detecting, in an analog manner, the amount of a probe which reacts with the capture immobilized in one spot. However, actually, such a procedure cannot be executed due to the restriction including, for example, the detection sensitivity of the detection equipment, the resolution, and the reaction efficiency. Therefore, the analog analysis can be performed by combining the plurality of spots, although the detection itself is performed in a digital manner with the plurality of spots having the different amounts of the capture immobilized per unit area of each of the spots on the base plate respectively for the captures of the identical type as performed in the present invention.
In still another aspect, the present invention lies in a biochip comprising a large number of spots based on capture solutions arranged on a base plate, obtained by supplying, onto the base plate, a plurality of types of the capture solutions each of which specifically reacts with a specimen and each of which is used to obtain information on a structure of the specimen; wherein the spots, which are composed of different types of the captures, are formed at an identical spot formation position. In this case, it is possible to greatly reduce the arrangement area for the spots, and it is possible to miniaturize the biochip itself.
In still another aspect, the present invention lies in a biochip comprising a large number of spots based on capture solutions arranged on a base plate, obtained by supplying, onto the base plate, a plurality of types of the capture solutions each of which specifically reacts with a specimen and each of which is used to obtain information on a structure of the specimen; wherein each of the spots has a shape of a substantially circular configuration, and a ratio between a major axis and a minor axis of the substantially circular configuration is not less than 0.9 and not more than 1.1.
Accordingly, the dispersion of the shape of each of the spots is reduced. It is easy to recognize the fluorescence light emission from the spot with a CCD camera or the like, and the inspection accuracy is improved. Especially, owing to the fact that the planar configuration of the spot is substantially circular, it is possible to avoid flowing the sample solution from the spot during the formation of the spot, and it is possible to prevent the sample solutions in the plurality of spots from being mixed with each other. In this case, it is also preferable that the spots are arranged at least in a zigzag configuration, and a ratio of an area in which the spot is not deposited with respect to an inspection effective area on the base plate is not more than 22%. In this case, it is possible to achieve a high degree of concentration of spots. Accordingly, it is possible to perform detailed genetic analysis for a large amount of a biochemical sample at once.
It is preferable for the biochip described above that the spots based on the sample solution are formed by means of an ink-jet system.
In the ink-jet system, the spot is formed by discharging the capture solution into the atmospheric air and allowing the capture solution to arrive at the base plate as a target. Therefore, the shape of the spot is a circular configuration which is approximate to a perfect circle owing to the surface tension of the sample. Therefore, the dispersion of the shape is reduced for the respective spots. Owing to the fact that the force of discharge and the number of times of discharge per unit time (discharge frequency) can be electrically controlled, the amount of the capture supplied to one spot on the base plate can be freely changed. Thus, the size of the spot and the amount of the capture per unit volume immobilized in the spot on the base plate can be varied.
Especially, the amount of the capture per unit volume is preferably varied by discharging and supplying the capture solution a plurality of times to one spot on the base plate in accordance with the ink-jet system. That is, the capture solution is discharged and supplied a plurality of times in a divided manner without discharging and supplying a large amount of the capture solution at once. Further, the discharge interval is adjusted so that a previously formed spot is not widened in spot diameter due to superimposition of the capture solution subsequently discharged. Accordingly, the amount of the capture supplied to the spot can be increased or decreased without changing the size of the spot. Thus, it is possible to vary the capture density per unit area.